PUBLICATIONS

Books:

1. Ferry, J. G. (ed.) 1993. Methanogenesis . Chapman and Hall, New York .

2. Ljungdahl, L. G., M. W. Adams, L. L. Barton, J. G. Ferry, and M. K. Johnson (ed.) 2003. Biochemistry and Physiology of Anaerobic Bacteria Springer-Verlag , New York .

Journal and review articles:

(* Denotes students)

1. Ferry, J. G., P. H. Smith, and R. S. Wolfe. 1974. Methanospirillum, a new genus of methanogenic bacteria, and characterization of Methanospirillum hungatii sp. nov. International Journal of Systematic Bacteriology 24:465-469.

2. Ferry, J. G., D. W. Sherod, H. D. Peck, Jr., and L. G. Ljungdahl. 1976. Levels of formyltetrahydrofolate synthetase and methylenetetrahydrofolate dehydrogenase in methanogenic bacteria, p.151-155. In H.G. Schlegel, G. Gottschalk, and N. Pfenning (ed.), Symposium on microbial production and utilization of Gases (H 2, CH 4, CO). E. Goltze K. G., Gottingen .

3. Ferry, J. G., and R. S. Wolfe. 1976. Anaerobic degradation of benzoate to methane by a microbial consortium. Archives for Microbiology 107:33-40.

4. Ferry, J.G., and R. S. Wolfe. 1977. Nutritional and biochemical characterization of Methanospirillum hungatii. Applied and Environmental Microbiology 34:371-376.

5. *Schauer, N. L., and J. G. Ferry. 1980. Metabolism of formate in Methanobacterium formicicum. Journal of Bacteriology 142:800-807.

6. *Schauer, N. L., and J. G. Ferry. 1982. Properties of formate dehydrogenase in Methanobacterium formicicum. Journal of Bacteriology 150:1-7.

7. *Schauer, N. L., *D. P. Brown, and J. G. Ferry. 1982. Kinetics of formate metabolism in Methanobacterium formicicum and Methanospirillum hungatei. Applied and Environmental Microbiology 44:549-554.

8. Barber, M. J., L. M. Siegel, *N. L. Schauer, *H. D. May, and J. G. Ferry. 1983. Formate dehydrogenase from Methanobacterium formicicum : electron paramagnetic resonance spectroscopy of the molybdenum and iron-sulfur centers. Journal of Biological Chemistry 258:10839-10845.

9. *Schauer, N. L., and J. G. Ferry. 1983. FAD requirement for the reduction of coenzyme F420 by formate dehydrogenase from Methanobacterium formicicum. Journal of Bacteriology 155:467-472.

10. *Sowers, K. R., and J. G. Ferry. 1983. Isolation and characterization of a methylotrophic marine methanogen, Methanococcoides methylutens gen. nov., sp. nov. Applied and Environmental Microbiology 45:684-690.

11. Ferry, J. G., and *K. R. Sowers. 1983. Principles of the microbial conversion of biomass to methane, p. 91-110.  In F. Zucconi, M. de Bertoldi, and S. Coppola (ed.), International symposium on biological reclamation of urban wastes, Naples.

12. *Dellinger, C. A., and J. G. Ferry. 1984. Effect of monensin on growth and methanogenesis of Methanobacterium formicicum. Applied and Environmental Microbiology 48:680-682.

13. *Lovley, D. R., R. C. Greening, and J. G. Ferry. 1984. Rapidly growing rumen methanogenic organism that synthesizes coenzyme M and has a high affinity for formate. Applied and Environmental Microbiology 48:81-87.

14. *Lovley, D. R., R. H. White, and J. G. Ferry. 1984. Identification of methyl coenzyme M as an intermediate in methanogenesis from acetate in Methanosarcina spp.  Journal of Bacteriology 160:521-525.

15. *Nelson, M. J. K., and J. G. Ferry. 1984. Carbon monoxide-dependent methyl coenzyme M methylreductase in acetotrophic Methanosarcina spp. Journal of Bacteriology 160:526-532.

16. *Nelson, M. J. K., *D. P. Brown, and J. G. Ferry. 1984. FAD requirement for the reduction of coenzyme F 420 by hydrogenase from Methanobacterium formicicum. Biochemical and Biophysical Research Communications 120:775-781.

17. *Sowers, K. R., *S. F. Baron, and J. G. Ferry. 1984. Methanosarcina acetivorans sp.nov., an acetotrophic methane-producing bacterium isolated from marine sediments. Applied and Environmental Microbiology 47:971-978.

18. *Sowers, K. R., J. L. Johnson, and J. G. Ferry. 1984. Phylogenetic relationships among the methylotrophic methane-producing bacteria and emendation of the family Methanosarcinaceae. International Journal of Systematic Bacteriology 34:444-450.

19. *Sowers, K. R., *M. J. K. Nelson, and J. G. Ferry. 1984. Growth of acetotrophic, methane-producing bacteria in a pH auxostat. Current Microbiology 11:227-230.

20. *Sowers, K. R., and J. G. Ferry. 1984. Characterization of a marine methanogenic consortium, p. 527-536. In Proceedings of the 1984 International Gas Research Conference. Government Institutes, Rockville .

21. *Lovley, D. R., and J. G. Ferry. 1985. Production and consumption of H 2 during growth of Methanosarcina spp. on acetate. Applied and Environmental Microbiology 49:247-249.

22. *Perez-Fillol, M., F. Rodriquez-Valera, and J. G. Ferry. 1985. Isolation of methanogenic bacteria able to grow in high salt concentration. Microbiologia 1:29-33.

23. *Sowers, K. R., and J. G. Ferry. 1985. Trace metal and vitamin requirements of Methanococcoides methylutens grown with trimethylamine. Archives for Microbiology 142:148-151.

24. Zinder, S. H., *K. R. Sowers, and J. G. Ferry. 1985. Methanosarcina thermophila sp. nov., a thermophilic, acetotrophic, methane-producing bacterium. International Journal of Systematic Bacteriology 35:522-523.

25. Ferry, J. G. 1985. Microbiological principles of methane formation from biomass. Food Engineering News. February:9-11.

26. *Schauer, N. L., and J. G. Ferry. 1986. Composition of the coenzyme F 420 -dependent formate dehydrogenase from Methanobacterium formicicum. Journal of Bacteriology 165:405-411.

27. *May, H. D., *N. L. Schauer, and J. G. Ferry. 1986. Molybdopterin cofactor from Methanobacterium formicicum formate dehydrogenase. Journal of Bacteriology 166:500-504.

28. Shuber, A. P., E. C. Orr, M. A. Recny, P. F. Schendel, *H. D. May, *N. L. Schauer, and J. G. Ferry. 1986. Cloning, expression, and nucleotide sequence of the formate dehydrogenase genes from Methanobacterium formicicum. Journal of Biological Chemistry 261:12942-12947.

29. *Schauer, N. L., J. G. Ferry, J. F. Honek, W. H. Orme-Johnson, and C. Walsh. 1986. Mechanistic studies of the coenzyme F420-reducing formate dehydrogenase from Methanobacterium formicicum. Biochemistry. 25:7163-7168.

30. *Terlesky, K. C., *M. J. K. Nelson, and J. G. Ferry. 1986. Isolation of an enzyme complex with carbon monoxide dehydrogenase activity containing corrinoid and nickel from acetate-grown Methanosarcina thermophila. Journal of Bacteriology 168:1053-1058.

31. Barber, M. J., *H. D. May, and J. G. Ferry. 1986. Inactivation of formate dehydrogenase from Methanobacterium formicicum by cyanide. Biochemistry 25:8150-8155.

32. *Baron, S. F., D. P. Brown, and J. G. Ferry. 1987. Locations of the hydrogenases of Methanobacterium formicicum after subcellular fractionation of cell extract. Journal of Bacteriology 169:3823-3825.

33. *Terlesky, K. C., M. J. Barber, *D. J. Aceti, and J. G. Ferry. 1987. EPR properties of the Ni-Fe-C center in an enzyme complex with carbon monoxide dehydrogenase activity from acetate-grown Methanosarcina thermophila. Evidence that acetyl-CoA is a physiological substrate. Journal of Biological Chemistry 262:15392-15395.

34. *Nelson, M. J. K., *K. C. Terlesky, and J. G. Ferry. 1987. Recent developments on the biochemistry of methanogenesis from acetate, p. 71-76. In H. W. van Verseveld and J. A. Duine (ed.), Microbial growth on C-1 compounds: Proceedings of the 5th international symposium. Martinus Nijhoff, Dordrecht.

35. *Baron, S. F., *H. D. May, *K. C. Terlesky, and J. G. Ferry. 1987. Metabolic regulation in methanogenic bacteria with potential influence on the performance of biomass digesters. Poultry Science 66:922-926.

36. *Terlesky, K. C., and J. G. Ferry. 1988. Ferredoxin requirement for electron transport from the carbon monoxide dehydrogenase complex to a membrane-bound hydrogenase in acetate-grown Methanosarcina thermophila. Journal of Biological Chemistry 263:4075-4079.

37. *Terlesky, K. C., and J. G. Ferry. 1988. Purification and characterization of a ferredoxin from acetate-grown Methanosarcina thermophila. Journal of Biological Chemistry 263:4080-4082.

38. Biavati, B., M. Vasta, and J. G. Ferry. 1988. Isolation and characterization of "Methanosphaera cuniculi " sp. nov. Applied and Environmental Microbiology 54:768-771.

39. Ortigues, I. , J. P. Fontenot, and J. G. Ferry. 1988. Digesta flows in sheep fed poor-quality hay supplemented with urea and carbohydrates. Journal of Animal Science. 66:975-985.

40. *May, H. D., *P. S. Patel, and J. G. Ferry. 1988. Effect of molybdenum and tungsten on synthesis and composition of formate dehydrogenase in Methanobacterium formicicum. Journal of Bacteriology 170:3384-3389.

41. *Patel, P. S., and J. G. Ferry. 1988. Characterization of the upstream region of the formate dehydrogenase operon of Methanobacterium formicicum. Journal of Bacteriology 170:3390-3395.

42. *Aceti, D. J., and J. G. Ferry. 1988. Purification and characterization of acetate kinase from acetate-grown Methanosarcina thermophila. Evidence for regulation of synthesis. Journal of Biological Chemistry 263:15444-15448.

43. *Haddock, J. D., and J. G. Ferry. 1989. Purification and characterization of phloroglucinol reductase from Eubacterium oxidoreducens. Journal of Biological Chemistry 264:4423-4427.

44. *Baron, S. F., D. S. Williams, *H. D. May, *P. S. Patel, H. C. Aldrich and J. G. Ferry. 1989. Immunogold localization of coenzyme F 420 -reducing formate dehydrogenase and coenzyme F420-reducing hydrogenase in Methanobacterium formicicum. Archives for Microbiology 151:307-313.

45. *Baron, S. F., and J. G. Ferry. 1989. Purification and properties of the membrane-associated coenzyme F420-reducing hydrogenase from Methanobacterium formicicum. Journal of Bacteriology 171:3846-3853.

46. *Baron, S. F., and J. G. Ferry. 1989. Reconstitution and properties of a coenzyme F420-mediated formate hydrogenlyase system in Methanobacterium formicicum. Journal of Bacteriology 171:3854-3859.

47. *Lundie, Jr. L. L., and J. G. Ferry. 1989. Activation of acetate by Methanosarcina thermophila: Purification and characterization of phosphotransacetylase. Journal of Biological Chemistry 264:18392-18396.

48. Ferry, J. G. 1989. Genus II. Methanospirillum, p. 2193-2195.  In N. Krieg and S. Holt (ed.), Bergey's manual of systematic bacteriology, Vol. III, 9th ed. The Williams and Wilkins Co., Baltimore.

49. *Sowers, K. R. 1989. Genus IV. Methanoccocoides, p. 2210-2211. In N. Krieg and S. Holt (ed.), Bergey's manual of systematic bacteriology, Vol. III, 9th ed. The Williams and Wilkins Co., Baltimore.

50. *Abbanat, D. R., *D. J. Aceti, *S. F. Baron, *K. C. Terlesky, and J. G. Ferry. 1989. Microbiology and biochemistry of the methanogenic archaeobacteria. Advances in Space Research 9:101-105.

51. *Jablonski, P. E., A. A. DiMarco, T. A. Bobik, *M. C. Cabell, and J. G. Ferry. 1990. Protein content and enzyme activities in methanol- and acetate-grown Methanosarcina thermophila. Journal of Bacteriology 172:1271-1275.

52. *Abbanat, D. R., and J. G. Ferry. 1990. Synthesis of acetyl coenzyme A by carbon monoxide dehydrogenase complex from acetate-grown Methanosarcina thermophila. Journal of Bacteriology 172:7145-7150.

53. Ferry, J. G. 1990. Formate dehydrogenase: microbiology, biochemistry and genetics, p. 117-141. In G. Codd, L. Dijkhuizen, and F.R. Tabita (ed.), Autotrophic microbiology and one-carbon metabolism. Kluwer Academic, Dordrecht.

54. Ferry, J. G. 1990. Formate dehydrogenase. Federation European Microbiological Society Reviews 87:377-382.

55. Raybuck, S. A., S. E. Ramer, *D. R. Abbanat, *J. W. Peters, W. H. Orme-Johnson, J. G. Ferry, and C. T. Walsh. 1991. Demonstration of carbon-carbon bond cleavage of acetyl-CoA using isotopic exchange catalyzed by the CO dehydrogenase complex from acetate-grown Methanosarcina thermophila. Journal of Bacteriology 173:929-932.

56. Johnson, J. L., N. R. Bastian, *N. L. Schauer, J. G. Ferry and K. V. Rajagopalan. 1991. Identification of molybdopterin guanine dinucleotide in formate dehydrogenase from Methanobacterium formicicum . Federation European Microbiological Society Letters 77:213-216.

57. *Jablonski, P. E., and J. G. Ferry. 1991. Purification and properties of methyl coenzyme M methylreductase from-acetate-grown Methanosarcina thermophila. Journal of Bacteriology 173:2481-2487.

58. *Abbanat, D. R., and J. G. Ferry. 1991. Resolution of component proteins in an enzyme complex from Methanosarcina thermophila catalyzing the synthesis or cleavage of acetyl-CoA. Proceedings of the National Academy of Sciences of the United States of America 88:3272-3276.

59. *Haddock, J. D., and J. G. Ferry. 1991. Anaerobic metabolism of aromatic compounds, p. 393- 416. In D.L. Wise (ed.), Bioprocessing and biotreatment of coal. Marcel Dekker, Inc., New York.

60. Ferry, J. G. 1992. Methane from acetate. Journal of Bacteriology 174:5489-5495.

61. Ferry, J. G. 1992. Biochemistry of methanogenesis. Critical Reviews in Biochemistry and Molecular Biology 27:473-503.

62. *White, W. B., and J. G. Ferry. 1992. Identification of formate dehydrogenase-specific mRNA species and nucleotide sequence of the fdhC gene of Methanobacterium formicicum. Journal of Bacteriology 174:4997-5004.

63. *Clements, A. P., and J. G. Ferry. 1992. Cloning, nucleotide sequence, and transcriptional analyses of the gene encoding a ferredoxin from Methanosarcina thermophila. Journal of Bacteriology 174:5244-5250.

64. *Jablonski, P. E., and J. G. Ferry. 1992. Reductive dechlorination of trichloroethylene by the CO-reduced CO dehydrogenase enzyme complex from Methanosarcina thermophila. FEMS Letters 96:55-60.

65. *Jablonski, P. E., W.-P. Lu, S. W. Ragsdale and J. G. Ferry. 1993. Characterization of the metal centers of the corrinoid/iron-sulfur component of the CO dehydrogenase enzyme complex from Methanosarcina thermophila by EPR spectroscopy and spectroelectrochemistry. Journal of Biological Chemistry 268:325-329.

66. *Haddock, J. D., and J. G. Ferry. 1993. Initial steps in the anaerobic degradation of 3,4,5-trihydroxybenzoate by Eubacterium oxidoreducens: characterization of mutants and the role of 1,2,3,5-tetrahydroxybenzene. Journal of Bacteriology 175:669-673.

67. *Clements, A. P., R. H. White, and J. G. Ferry. 1993. Structural characterization and physiological function of component B from Methanosarcina thermophila. Archives of Microbiology 159:296-300.

68. *Latimer, M. T., and J. G. Ferry. 1993. Cloning, sequence analysis, and hyperexpression of the genes encoding phosphotransacetylase and acetate kinase from Methanosarcina thermophila. Journal of Bacteriology 175:6822-6829.

69. *Alber, B. E., *A. P. Clements, *P. E. Jablonski, *M. T. Latimer, and J. G. Ferry. 1993. Enzymology of the methanogenic fermentation of acetate by Methanosarcina thermophila, p. 163-170. In C. Murrell and D. Kelly (eds.), Microbial growth on C1 compounds. Intercept, Ltd., Andover.

70. Ferry, J. G. 1993. Fermentation of acetate, p. 304-334. In J. G. Ferry (ed.), Methanogenesis. Chapman and Hall, New York.

71. *Lu, W.-P., *P. E. Jablonski, *M. Rasche, J. G. Ferry, and S. W. Ragsdale. 1994. Characterization of the metal centers of the Ni/Fe-S component of the CO dehydrogenase enzyme complex from Methanosarcina thermophila. Journal of Biological Chemistry 269:9736-9742.

72. *Alber, B. E., and J. G. Ferry. 1994. A carbonic anhydrase from the archaeon Methanosarcina thermophila. Proceedings of the National Academy of Sciences of the United States of America 91:6909-6913.

73. *Clements, A. P., L. Kilpatrick, W.-P. Lu, S. W. Ragsdale, and J. G. Ferry. 1994. Characterization of the iron-sulfur clusters in ferredoxin from acetate-grown Methanosarcina thermophila. Journal of Bacteriology 176:2689-2693.

74. *Peer, C. W., *M. H. Painter, *M. E. Rasche, and J. G. Ferry. 1994. Characterization of a CO:heterodisulfide oxidoreductase system from acetate-grown Methanosarcina thermophila. Journal of Bacteriology 176:6974-6979.

75. Ferry, J. G. 1994. CO Dehydrogenase of methanogens, p. 539-556. In H.L. Drake (ed.), Acetogenesis. Chapman and Hall, New York.

76. *Singh-Wissmann, K., and J. G. Ferry. 1995. Transcriptional regulation of the phosphotransacetylase-encoding and acetate kinase-encoding genes ( pta and ack ) from Methanosarcina thermophila. Journal of Bacteriology 177:1699-1702.

77. *Maupin-Furlow, J. A., and J.G. Ferry. 1995. A proteasome from the methanogenic archaeon Methanosarcina thermophila. Journal of Biological Chemistry 270:28617-28622.

78. *Schauer, N. L., and J. G. Ferry. 1995. Purification of formate dehydrogenase from Methanobacterium formicicum, p. 221-224. In F.T. Robb, A.R. Place, K.R. Sowers, H.J. Schreier, S. DasSarma and E.M. Fleischmann (ed.), Archaea, a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

79. *Baron, S. F., and J. G. Ferry. 1995. Purification of the coenzyme F420-reducing hydrogenase from Methanobacterium formicicum, p. 217-220. In F. T. Robb, A. R. Place, K. R. Sowers, H. J. Schreier, S. DasSarma and E. M. Fleischmann (ed.), Archaea, a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

80. *Latimer, M. T., and J. G. Ferry. 1995. Purification of Methanosarcina thermophila acetate kinase and phosphotransacetylase overproduced in Escherichia coli, p. 225-230. In F.T. Robb, A.R. Place, K.R. Sowers, H.J. Schreier, S. DasSarma and E.M. Fleischmann (ed.), Archaea, a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

81. *Clements, A. P., and J. G. Ferry. 1995. Purification of the carbon monoxide dehydrogenase-linked ferredoxin from Methanosarcina thermophila, p. 237-242. In F. T. Robb, A. R. Place, K. R. Sowers, H. J. Schreier, S. DasSarma and E. M. Fleischmann (ed.), Archaea, a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York .

82. *Rasche, M. E., *K. C. Terlesky, *D. R. Abbanat, and J. G. Ferry. 1995. Purification of carbon monoxide dehydrogenase from Methanosarcina thermophila, p. 231-236. In F.T. Robb, A.R. Place , K.R. Sowers, H.J. Schreier, S. DasSarma and E.M. Fleischmann (ed.), Archaea, a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

83. *Alber, B. E., and J. G. Ferry. 1995. Purification of carbonic anhydrase from Methanosarcina thermophila, p. 243-246. In F.T. Robb, A.R. Place, K.R. Sowers, H.J. Schreier, S. DasSarma and E.M. Fleischmann (ed.), Archaea, a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

84. Ferry, J. G. 1995. CO dehydrogenase. Annual Reviews of Microbiology. 49:305-333.

85. *Maupin-Furlow, J., and J. G. Ferry. 1996. Characterization of the cdhD and cdhE genes encoding subunits of the corrinoid/iron-sulfur enzyme of the CO dehydrogenase complex from Methanosarcina thermophila. Journal of Bacteriology 178:340-346.

86. Ferry, J. G. and *J. A. Maupin-Furlow. 1996. Analysis of genes in the pathway for the fermentation of acetate to methane by Methanosarcina thermophila, p. 64-71. In M. Lidstrom, and R. Tabita (ed.), Microbial growth on C1 compounds. Kluwer Academic, Dordrecht .

87. *Alber, B. E., and J. G. Ferry. 1996. Characterization of heterologously produced carbonic anhydrase from Methanosarcina thermophila. Journal of Bacteriology. 178:3270-3274.

88. Kisker, C., H. Schindelin, *B. E. Alber, J. G. Ferry, and D. C. Rees. 1996. A left-handed ß-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila. EMBO Journal. 15:2323-2330.

89. *Jablonski, P. E., *D. J. Pheasant, and J. G. Ferry. 1996. Coversion of kepone by Methanosarcina thermophila. FEMS Letters. 139:169-173.

90. *Rasche, M. E., and J. G. Ferry. 1996. Molecular biology of methanogens and Archaea. p. 66-78. In R.A. Meyers (ed.), The Encyclopedia of Molecular Biology and Molecular Medicine. Weinheim, New York.

91. *Latimer, M. T., *M. H. Painter, and J. G. Ferry. 1996. Characterization of an iron-sulfur flavoprotein from Methanosarcina thermophila. Journal of Biological Chemistry. 271:24023-24028.

92. *Maupin-Furlow, J. A., and J. G. Ferry. 1996. Analysis of the CO dehydrogenase/acetyl-CoA synthase operon of Methanosarcina thermophila. Journal of Bacteriology 178:6849-6856.

93. Ferry, J. G. 1997. Enzymology of the fermentation of acetate to methane by Methanosarcina thermophila. BioFactors 6:25-35.

94. Ferry, J. G. 1997. Methane: small molecule, big impact. Science 278:1413-1414.

95. Rasche, M. E., *K. S. Smith, and J. G. Ferry. 1997. Identification of cysteine and arginine residues essential for the phosphotransacetylase from Methanosarcina thermophila. Journal of Bacteriology 179:7712-7717.

96. Buss, K. A., *C. Ingram-Smith, J. G. Ferry, D. A. Sanders, and M. S. Hasson. 1997. Crystallization of acetate kinase from Methanosarcina thermophila and prediction of its fold. Protein Science 6:2659-2662.

97. *Singh-Wissmann, K., *C. Ingram-Smith, *R. D. Miles, and J. G. Ferry. 1998. Identification of essential glutamates in the acetate kinase from Methanosarcina thermophila. Journal of Bacteriology 180:1129-1134.

98. *Maupin-Furlow, J. A., H. C. Aldrich, and J. G. Ferry. 1998. Biochemical characterization of the 20S proteasome from the methanoarchaeaon Methanosarcina thermophila. Journal of Bacteriology 180:1480-1487.

99. Becker, D. F., *U. Leartsakulpanich, K. K. Surerus, J. G. Ferry, and S. W. Ragsdale. 1998. Electrochemical and spectroscopic properties of the iron-sulfur flavoprotein from Methanosarcina thermophila. Journal of Biological Chemistry 273:26462-26469.

100. Ferry, J. G. 1999. Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiological Reviews 23:13-38.

101. *Smith, K. S., and J. G. Ferry. 1999. A plant-type ( b class) carbonic anhydrase in the thermophilic methanoarchaeon Methanobacterium thermoautotrophicum. Journal of Bacteriology 181:6247-6253.

102. *Alber, B. E., C. M. Colangelo, J. Dong, C. M. V. Stålhandske, T. T. Baird, C. Tu, C. A. Fierke, D. N. Silverman, R. A. Scott, and J. G. Ferry. 1999. Kinetic and spectroscopic characterization of the gamma carbonic anhydrase from the methanoarchaeon Methanosarcina thermophila. Biochemistry 38:13119-13128.

103. *Smith, K. S., *C. Jakubzick, T. S. Whittam, and J. G. Ferry. 1999. Carbonic anhydrase is an ancient enzyme widespread in prokaryotes. Proceedings of the National Academy of Sciences USA 96:15184-15189.

104. *Borup, B., and J. G. Ferry. 2000. O -Acetylserine sulfhydrylase from Methanosarcina thermophila. Journal of Bacteriology 182:45-50.

105. *Liermann, L. J., B. E. Kalinowski, S. L. Brantley, and J. G. Ferry. 2000. Role of bacterial siderophores in dissolution of hornblende. Geochimica et Cosmochimica Acta. 64:587-602.

106. *Singh-Wissmann, K., *R. D. Miles, *C. Ingram-Smith, and J. G. Ferry. 2000. Identification of essential arginines in the acetate kinase from Methanosarcina thermophila. Biochemistry 39:3671-3677.

107. Iverson, T. M., *B. E. Alber, C. Kisker, J. G. Ferry, and D. C. Rees. 2000. A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. Biochemistry 39:9222-9231.

108. *Tripp, B. C., and J. G. Ferry. 2000. A structure-function study of a proton transport pathway in the gamma-class carbonic anhydrase from Methanosarcina thermophila. Biochemistry 39:9232-9240.

109. *Borup, B., and J. G. Ferry. 2000. Cysteine biosynthesis in the Archaea: Methanosarcina thermophila utilizes O- acetylserine sulfhydrylase. FEMS Microbiology Letters 189:205-210.

110. *Smith, K. S., and J. G. Ferry. 2000. Procaryotic carbonic anhydrases. FEMS Microbiological Reviews 24:335-366.

111. *Leartsakulpanich, U., M. L. Antonkine, and J. G. Ferry. 2000. Site-specific mutational analysis of a novel cysteine motif proposed to ligate the 4Fe-4S cluster in the iron-sulfur flavoprotein (Isf) of the thermophilic methanoarchaeon Methanosarcina thermophila. Journal of Bacteriology 182:5309-5316.

112. *Ingram-Smith, C., *R. D. Barber, and J. G. Ferry. 2000. The role of histidines in the acetate kinase from Methanosarcina thermophila. Journal of Biological Chemistry 275:33765-33700.

113. *Smith, K. S., N. J. Cosper, C. Stalhandske, R. A. Scott, and J. G. Ferry. 2000. Structural and kinetic characterization of an archaeal ß-class carbonic anhydrase. Journal of Bacteriology 182:6605-6613.

114. Buss, K. A., D. R. Cooper, *C. Ingram-Smith, J. G. Ferry, D. A. Sanders, and M. S. Hasson. 2001. Urkinase: Structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases. Journal of Bacteriology 183:680-686.

115. Strop, P., *K. S. Smith, T. M. Iverson, J. G. Ferry, and D. C. Rees. 2001. Crystal structure of the “cab”-type beta class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum. Journal of Biological Chemistry 276:10299-10305.

116. *Barber, R. D., and J. G. Ferry. 2001. Archaeal proteasomes. Methods in Enzymology 330:413-424.

117. *Iyer, P. P., and J. G. Ferry. 2001. Role of arginines in coenzyme A binding and catalysis by the phosphotransacetylase from Methanosarcina thermophila. Journal of Bacteriology 183:4244-4250.

118. Tu, C., *B. C. Tripp, J. G. Ferry, and D. N. Silverman. 2001. Bicarbonate as proton donor in catalysis by Zn(II)- and Co(II)-containing carbonic anhydrases. Journal of the American Chemical Society 123:5861-5866.

119. Ferry, J. G., and D. R. Boone. 2001. Genus I. Methanospirillum , p. 264-267.  In R. Castenholtz and D.R. Boone (eds.), Bergey's manual of systematic bacteriology, Vol. I, 2nd ed. The Williams and Wilkins Co., Baltimore.

120. *Zhao, T., *F. Cruz, and J. G. Ferry. 2001. Iron-sulfur flavoprotein (Isf) from Methanosarcina thermophila is the prototype of a widely distributed family. Journal of Bacteriology 183:6225-6233.

121. *Tripp, B.C., *K. S. Smith, and J. G. Ferry. 2001. Carbonic anhydrase: new insights for an ancient enzyme. Journal of Biological Chemistry 276:48615-48618.

122. *Miles, R. D., *P. P. Iyer, and J. G. Ferry. 2001. Site-directed mutational analysis of active site residues in the acetate kinase from Methanosarcina thermophila. Journal of Biological Chemistry 276:45059-45064.

123. Ferry, J. G. 2001. Methanogenesis Biochemistry. Encyclopedia of Life Sciences, Nature Publishing Group, London . [Online.] www.els.net .

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125. *Tripp, B. C., C. Tu, and J. G. Ferry. 2002. Role of arginine 59 in the ?-class carbonic anhydrases. Biochemistry 41:669-678.

126. Galagan, J. E., C. Nusbaum, A. Roy, M. G. Endrizzi, P. Macdonald, W. FitzHugh, S. Calvo, R. Engels, S. Smirnov, D. Atnoor, A. Brown, N. Allen, J. Naylor, N. Stange-Thomann, K. DeArellano, R. Johnson, L. Linton, P. McEwan, K. McKernan, J. Talamas, A. Tirrell, W. Ye, A. Zimmer, *R. D. Barber, I. Cann, D. E. Graham, D. A. Grahame, A. Guss, R. Hedderich, *C. Ingram-Smith, H. C. Kuettner, J. A. Krzycki, J. A. Leigh, W. Li, J. Liu, B. Mukhopadhyay, J. N. Reeve, *K. Smith, T. Springer, L. A. Umayam, O. White, R. H. White, E. Conway de Macario, J. G. Ferry, K. F. Jarrell, H. Jing, A. J. L. Macario, I. Paulsen, M. Pritchett, K. R. Sowers, R. V. Swanson, S. H. Zinder, E. Lander, W. W. Metcalf, and B. Birren. 2002. The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity. Genome Research 12:532-542.

127. Sowers, K. R., and J. G. Ferry. 2002. Methanogenesis in the marine environment, p. 1913-1923. In G. Bitton (ed.), The Encyclopedia of Environmental Microbiology. John Wiley & Sons, Inc.

128. *Miles, R. D., *A. Gorrell, and J. G. Ferry. 2002. Evidence for a transition state analog, MgADP-aluminum fluoride-acetate, in acetate kinase from Methanosarcina thermophila. Journal of Biological Chemistry 277:22547-22552.

129. *Smith, K. S., *C. Ingram-Smith, and J. G. Ferry. 2002. Roles of the conserved aspartate and arginine in the catalytic mechanism of an archaeal ß- class carbonic anhydrase. Journal of Bacteriology 184:4240-4245.

130. *Ding, Y.-H. R., S.-P. Zhang, J.-F. Tomb, and J. G. Ferry. 2002. Genomic and proteomic analyses reveal multiple homologs of genes encoding enzymes of the methanol:coenzyme M methyltransferase system that are differentially expressed in methanol- and acetate-grown Methanosarcina thermophila. FEMS Microbiology Letters 215:127-132.

131. Tu, C., R. S. Rowlett, *B. C. Tripp, J. G. Ferry, and D. N. Silverman. 2002. Chemical rescue of proton transfer in catalysis by carbonic anhydrases in the beta and gamma class. Biochemistry 41:15429-15435.

132. Ferry, J. G. 2003. One-carbon metabolism in methanogenic anaerobes, p. 143-156. In L. G. Ljungdahl, M. W. Adams, L. L. Barton, J. G. Ferry, and M. K. Johnson (ed.), Biochemistry and Physiology of Anaerobic Bacteria. Springer-Verlag , New York .

133. *Iyer, P. P., *S. H. Lawrence, H. P. Yennawar, and J. G. Ferry. 2003. Expression, purification, crystallization and preliminary X-ray analysis of phosphotransacetylase from Methanosarcina thermophila. Acta Crystallographica Section D, Biological Crystallography 59:1517-20.

134. *Ding, Y.-H. R., and J. G. Ferry. 2004. Flavin mononucleotide-binding flavoprotein family in the domain Archaea. Journal of Bacteriology 186:90-97.

135. *Tripp, B. C., *C. B. Bell III, *F. Cruz, C. Krebs, and J. G. Ferry. 2004. A role for iron in an ancient carbonic anhydrase. Journal of Biological Chemistry 279:6683-6687.

136. *Iyer, P. P., *S. H. Lawrence, K. B. Luther, K. R. Rajashankar, H. P. Yennawar, J. G. Ferry, and H. Schindelin. 2004. Crystal Structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila. Structure 12:559-567.

137. Innocenti, A., *S. Zimmerman, J. G. Ferry, A. Scozzafava, and C. T. Supuran. 2004. Carbonic anhydrase inhibitors. Inhibition of the zinc and cobalt ?-class enzyme from the archaeon Methanosarcina thermophila with anions. Bio-organic and Medicinal Chemistry Letters 14:3327-3331.

138. Innocenti, A., *S. Zimmerman, J. G. Ferry, A. Scozzafava, and C. T. Supuran. 2004. Carbonic anhydrase inhibitors. Inhibition of the beta-class enzyme from the methanoarchaeon Methanobacterium thermoautotrophicum (Cab) with anions. Bio-organic and Medicinal Chemistry Letters 14:4563-4567.

139. *Zimmerman, S., A. Innocenti, A. Casini, J. G. Ferry, A. Scozzafava, and C. T. Supuran. 2004. Carbonic anhydrase inhibitors. Inhibition of the prokariotic beta and gamma-class enzymes from Archaea with sulfonamides. Bioorganic and Medicinal Chemistry Letters 14:6001-6006.

140. Parisi, G., M. Perales, M. S. Fornasari, A. Colaneri, N. González-Schain, D. Gómez-Casati, *S. Zimmermann, A. Brennicke, A. Araya, J. G. Ferry, J. Echave, and E. Zabaleta. 2004. Gamma carbonic anhydrases in plant mitochondria. Plant Molecular Biology 55:193-207.

141. *Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry. 2005. Proteome of Methanosarcina acetivorans . Part I: an expanded view of the biology of the cell. Journal of Proteome Research 4:112-128.

142. *Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry. 2005. Proteome of Methanosarcina acetivorans . Part II: comparison of protein levels in acetate- and methanol-grown cells. Journal of Proteome Research 4:129-135.

143. *Gorrell, A., *S. H. Lawrence, and J. G. Ferry. 2005. Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila. Journal of Biological Chemistry 280:10731-10742.

144. *Ingram-Smith, C., *A. Gorrell, *S. H. Lawrence, *P. Iyer, *K. Smith, and J. G. Ferry. 2005. Characterization of the acetate binding pocket in the Methanosarcina thermophila acetate kinase. Journal of Bacteriology 187:2386-2394.

145. Rasche, M. E., and J. G. Ferry. 2005. Methanogens and the archaebacteria, molecular biology of, p. 237-261. In R. A. Meyers (ed.), Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2nd ed, vol. 8. Wiley-VCH Verlag GmbH & Co., Weinheim.

146. *Iyer, P., and J. G. Ferry. 2005. Acetate kinase from Methanosarcina thermophila , a key enzyme for methanogenesis, p. 239-246. In J. L. Barredo (ed.), Microbial Enzymes and Biotransformations, vol. 17. Humana Press Inc., Totowa , NJ .

147. Moran, J. J., C. H. House, K. H. Freeman, and J. G. Ferry. 2005. Trace methane oxidation studied in several Euryarchaeota under diverse conditions. Archaea 1:303-309.

148. Andrade, S. L. A, *F. Cruz, C. L. Drennan, V. Ramakrishnan, D. C. Rees, J. G. Ferry, and O. Einsle. 2005. Structures of the iron-sulfur flavoproteins from Methanosarcina thermophila and Archaeoglobus fulgidus. Journal of Bacteriology 187:3848-3854.

149. *Li, Q., L. Li, T. Rejtar, *D. J. Lessner, B. L. Karger, and J. G. Ferry. 2006. Electron transport in the pathway of acetate conversion to methane in the marine archaeon Methanosarcina acetivorans. Journal of Bacteriology 188:702-710.

150. *Lawrence, S. H., K. B. Luther, H. Schindelin, and J. G. Ferry. 2006. Structural and functional studies suggest a catalytic mechanism for the phosphotransacetylase from Methanosarcina thermophila. Journal of Bacteriology 188:1143-1154.

151. *Lawrence, S. H., and J. G. Ferry. 2006. Steady-state kinetic analysis of phosphotransacetylase from Methanosarcina thermophila. Journal of Bacteriology 188:1155-1158.

152. *Cruz, F., and J. G. Ferry. 2006. Interaction of iron-sulfur flavoprotein with oxygen and hydrogen peroxide. Biochimica et Biophysica Acta. 1760:858-864.

153. *Patridge, E. V., and J. G. Ferry. 2006. WrbA from Escherichia coli and Archaeoglobus fulgidus is an NAD(P)H:quinone oxidoreductase. Journal of Bacteriology 188:3498-3506.

154. Ferry, J. G., and C. H. House. 2006. The stepwise evolution of early life driven by energy conservation. Molecular Biology and Evolution 23:1286-1292.

155. *Zimmerman, S. A., and J. G. Ferry. 2006. Proposal for a hydrogen bond network in the active site of the prototypic gamma-class carbonic anhydrase. Biochemistry 45:5149-5157.

156. Andreev, V. P., L. Li, T. Rejtar, Q. Li, J. G. Ferry, and B. L. Karger. 2006. A new algorithm for 15N/14N quantitation with LC-ESI-MS using LTQ-FT mass spectrometry. Journal of Proteome Research 5:2039-2045.

157. *Lessner, D. J., L. Li, *Q. Li, T. Rejtar, V. P. Andreev, *M. Reichlen, *K. Hill, J. J. Moran, B. L. Karger, and J. G. Ferry. 2006. An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics. Proceedings of the National Academy of Sciences 103:17921-17926.

158. Ferry, J. G., and *K. A. Kastead. 2007. Methanogenesis. p. 288-314. In R. Cavicchioli (ed.), Archaea: Molecular Cell Biology. ASM Press, Washington , D.C.

159. Li, L., *Q. Li, L. Rohlin, U. Kim, K. Salmon, T. Rejtar, R. P. Gunsalus, B. L. Karger, and J. G. Ferry. 2007. Quantitative proteomic and microarray anaylsis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol. Journal of Proteome Research 6:759-771.

160. Hausrath, E. M., L. J. Liermann, C. H. House, J. G. Ferry, and S. L. Brantley. 2007. The effect of methanogen growth on mineral substrates: will Ni markers of methanogen-based communities be detectable in the rock record? Geobiology 5:49-61.

161. *Zimmerman, S. A., J. G. Ferry, and C. Supuran. 2007. Inhibition of the archaeal beta-class (Cab) and gamma-class ( Cam ) carbonic anhydrases. Current Topics in Medicinal Chemistry 7:901-909.

162. *Lessner, D. J. & J. G. Ferry. 2007. The Archaeon Methanosarcina acetivorans Contains a Protein Disulfide Reductase with an Iron-Sulfur Cluster. Journal of Bacteriology 189:7475-7484.

163. Andrade, S. L. A., E. V. Patridge, J. G. Ferry and O. Einsle. 2007. Crystal structure of the NADH:quinone oxidoreductase WrbA from Escherichia coli. Journal of Bacteriology 189:9101-9107.

164. *Gorrell, A. and J. G. Ferry. 2007. Investigation of the Methanosarcina thermophila acetate kinase mechanism by fluorescence quenching. Biochemistry 46:14170-14176.

165. Ferry, J. G. 2007. Acetate Based Methane Production. p. xxx-xxx. In Wall, J., C. S. Harwood and A. Demain, (eds.), Biofuels. ASM Press, Washington D. C. (in press).

166. Ferry, J. G. and D. J. Lessner*. 2008. Methanogenesis in Marine Sediments. p. 147-157. In Wiegel, J., R. Maier and M. W. W. Adams (eds.), Incredible Anaerobes: From Physiology to Genomics to Fuels, Annals of the New York Academy of Sciences, New York, NY.